If it is what I think it is, (and what I'm thinking of aired one afternoon on Nickelodeon), I recall the characters standing around "Muppet Central" with loads of TV screens around, and we learn about the fancy pupptry work they've done over the years (including detailed synopses on how the Gorgs and Doozers work, plus how they did all the bike riding scenes over the first few films, which was the first time I heard of Brian Henson). For the denoument, they went to bluescreen and pulled back to show the puppeteers working the main characters. Once back in the fantasy world, Fozzie makes an oath never to look down again. Kermit (and I believe Scooter was there as well, which if so would have made it earlier than 1994) do so anyway, see just the floor, and breath huge sighs of relief that it was all just a bad dream that humans were manipulating them (or so they think...)
Sound familiar to anyone?